SAMOVA (Spatial Analysis of MOlecular VAriance) implements an approach to define groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims at maximizing the proportion of total genetic variance due to differences between groups of populations
AlphaSeqOpt is a software package for determining the optimum distribution of sequencing resources within a population of interest. AlphaSeqOpt determines which individuals should be prioritised for sequencing and the total investment to be made in sequencing this individual. The aim of the algorithm is to capture, sequence and phase as many of the population haplotypes as possible for maximum sequence imputation ability into the rest of the population.
AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. Focal individuals can be descendants of a bi-parental cross at various levels of selfing or can be parents of one or more bi-parental populations. All information on the model of analysis, input files and their layout, is specified in a single parameter file.
AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling.
BioBin meets a critical need for an improved binning algorithm through the advantage of prior biological knowledge and potential cumulative effects of biologically aggregated RVs. BioBin requires the Library of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data. BioBin can be used to apply multiple levels of burden collapsing/testing, including: regulatory regions, evolutionary conserved regions, genes, and/or pathways without a need for an external feature file. BioBin aids rare variant analysis by binning variants according to prior biological knowledge.